Separation and records
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The requirement
A facility handling both mammalian and non-mammalian protein maintains separate equipment, or uses "clean-out procedures or other means adequate to prevent carry-over".
Adequate is a standard, not a number
The regulation names the outcome, preventing carry-over, rather than prescribing a method. That puts the burden on you to show the method you chose achieves it.
Written procedures, receipt through shipment
Not just the mixing step. Intake, storage, conveying, mixing, packing and despatch are all places carry-over happens, and the procedures cover the whole path.
Records for at least a year
Receipt, processing and distribution. Purchase invoices and copies of labeling available for inspection. Test results and certifications available too.
Which favours one decision for a small operation
Handle one or the other. A facility that never takes in prohibited mammalian protein has no separation problem to solve and no clean-out to validate, and that is a far cheaper position than proving adequacy.
Shared or contract manufacturing needs this answered first
If somebody else blends for you, their separation practice becomes your exposure. Ask what they handle and how they separate it before the first production run rather than after a question arises.
The exemption route exists and is narrow
The regulation contemplates exemption where validated deactivation, validated testing or an approved marking system is used. Those are specific mechanisms rather than a general argument that your process is careful.
Write down why your method is adequate
The regulation asks for an outcome and leaves the method to you, which means the reasoning is the evidence. A note saying which step carries the risk, what you do about it and why that is sufficient is worth more than a procedure that only lists actions.
Sequence is a control in itself
Running the non-mammalian products first after a clean-down, and the prohibited-protein products last before one, reduces how often carry-over can matter at all. It costs scheduling rather than equipment.